Starting phenix.real_space_refine on Mon Feb 10 20:32:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kom_62478/02_2025/9kom_62478.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kom_62478/02_2025/9kom_62478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kom_62478/02_2025/9kom_62478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kom_62478/02_2025/9kom_62478.map" model { file = "/net/cci-nas-00/data/ceres_data/9kom_62478/02_2025/9kom_62478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kom_62478/02_2025/9kom_62478.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1485 2.51 5 N 377 2.21 5 O 396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2268 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2268 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 4 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Time building chain proxies: 2.44, per 1000 atoms: 1.08 Number of scatterers: 2268 At special positions: 0 Unit cell: (60.48, 50.4, 119.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 396 8.00 N 377 7.00 C 1485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 242 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 266.1 milliseconds 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 568 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 69.8% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 Proline residue: A 46 - end of helix removed outlier: 4.291A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 104 through 109 removed outlier: 4.443A pdb=" N LYS A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 3.545A pdb=" N ALA A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 132 through 159 removed outlier: 3.825A pdb=" N ARG A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.991A pdb=" N LEU A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 231 removed outlier: 3.809A pdb=" N ASN A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 removed outlier: 3.592A pdb=" N PHE A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 265 through 294 removed outlier: 3.967A pdb=" N VAL A 284 " --> pdb=" O TYR A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 4.574A pdb=" N LEU A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.634A pdb=" N LYS A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.295A pdb=" N GLY A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 137 hydrogen bonds defined for protein. 408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.56 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 698 1.34 - 1.46: 559 1.46 - 1.58: 1048 1.58 - 1.70: 0 1.70 - 1.81: 13 Bond restraints: 2318 Sorted by residual: bond pdb=" CB GLU A 193 " pdb=" CG GLU A 193 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CB GLU A 252 " pdb=" CG GLU A 252 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CB TYR A 151 " pdb=" CG TYR A 151 " ideal model delta sigma weight residual 1.512 1.535 -0.023 2.20e-02 2.07e+03 1.05e+00 bond pdb=" CB ASP A 148 " pdb=" CG ASP A 148 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.68e-01 bond pdb=" C TRP A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.41e-01 ... (remaining 2313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 3063 1.82 - 3.65: 58 3.65 - 5.47: 14 5.47 - 7.30: 14 7.30 - 9.12: 2 Bond angle restraints: 3151 Sorted by residual: angle pdb=" CA GLU A 193 " pdb=" CB GLU A 193 " pdb=" CG GLU A 193 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA TYR A 151 " pdb=" CB TYR A 151 " pdb=" CG TYR A 151 " ideal model delta sigma weight residual 113.90 120.40 -6.50 1.80e+00 3.09e-01 1.30e+01 angle pdb=" CB MET A 121 " pdb=" CG MET A 121 " pdb=" SD MET A 121 " ideal model delta sigma weight residual 112.70 121.82 -9.12 3.00e+00 1.11e-01 9.25e+00 angle pdb=" CA GLU A 252 " pdb=" CB GLU A 252 " pdb=" CG GLU A 252 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.88e+00 angle pdb=" CB GLU A 252 " pdb=" CG GLU A 252 " pdb=" CD GLU A 252 " ideal model delta sigma weight residual 112.60 117.60 -5.00 1.70e+00 3.46e-01 8.65e+00 ... (remaining 3146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 1135 16.00 - 32.01: 185 32.01 - 48.01: 60 48.01 - 64.01: 10 64.01 - 80.02: 3 Dihedral angle restraints: 1393 sinusoidal: 528 harmonic: 865 Sorted by residual: dihedral pdb=" CA GLU A 252 " pdb=" C GLU A 252 " pdb=" N THR A 253 " pdb=" CA THR A 253 " ideal model delta harmonic sigma weight residual 180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 dihedral pdb=" N ASN A 152 " pdb=" CA ASN A 152 " pdb=" CB ASN A 152 " pdb=" CG ASN A 152 " ideal model delta sinusoidal sigma weight residual -60.00 -116.98 56.98 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA HIS A 203 " pdb=" C HIS A 203 " pdb=" N SER A 204 " pdb=" CA SER A 204 " ideal model delta harmonic sigma weight residual -180.00 -164.71 -15.29 0 5.00e+00 4.00e-02 9.35e+00 ... (remaining 1390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 233 0.030 - 0.060: 89 0.060 - 0.090: 40 0.090 - 0.120: 15 0.120 - 0.150: 4 Chirality restraints: 381 Sorted by residual: chirality pdb=" CA SER A 45 " pdb=" N SER A 45 " pdb=" C SER A 45 " pdb=" CB SER A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA TRP A 105 " pdb=" N TRP A 105 " pdb=" C TRP A 105 " pdb=" CB TRP A 105 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 378 not shown) Planarity restraints: 383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 193 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" CD GLU A 193 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 193 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 193 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 252 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" CD GLU A 252 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A 252 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 252 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 105 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 106 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " -0.022 5.00e-02 4.00e+02 ... (remaining 380 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 509 2.78 - 3.31: 2115 3.31 - 3.84: 3654 3.84 - 4.37: 3531 4.37 - 4.90: 6478 Nonbonded interactions: 16287 Sorted by model distance: nonbonded pdb=" OH TYR A 224 " pdb=" OG1 THR A 281 " model vdw 2.245 3.040 nonbonded pdb=" O PRO A 322 " pdb=" ND2 ASN A 327 " model vdw 2.308 3.120 nonbonded pdb=" N GLU A 238 " pdb=" OE1 GLU A 238 " model vdw 2.313 3.120 nonbonded pdb=" OD1 ASP A 35 " pdb=" ND2 ASN A 290 " model vdw 2.330 3.120 nonbonded pdb=" O ARG A 156 " pdb=" NE2 GLN A 159 " model vdw 2.334 3.120 ... (remaining 16282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.150 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2318 Z= 0.251 Angle : 0.786 9.122 3151 Z= 0.400 Chirality : 0.042 0.150 381 Planarity : 0.004 0.039 383 Dihedral : 17.934 80.018 819 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.81 % Allowed : 41.13 % Favored : 58.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.52), residues: 281 helix: 1.05 (0.39), residues: 189 sheet: -1.11 (1.37), residues: 18 loop : -1.55 (0.72), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 297 HIS 0.001 0.000 HIS A 90 PHE 0.018 0.002 PHE A 189 TYR 0.009 0.001 TYR A 280 ARG 0.000 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.264 Fit side-chains REVERT: A 29 ARG cc_start: 0.6910 (ttm-80) cc_final: 0.6607 (ttp-110) REVERT: A 129 GLN cc_start: 0.6987 (tp40) cc_final: 0.6477 (tt0) REVERT: A 194 ARG cc_start: 0.6344 (mtm-85) cc_final: 0.5518 (tmt170) REVERT: A 201 ARG cc_start: 0.7109 (mmm-85) cc_final: 0.6291 (ttm110) REVERT: A 237 GLN cc_start: 0.7236 (tp40) cc_final: 0.6987 (tp40) REVERT: A 239 GLU cc_start: 0.8092 (pt0) cc_final: 0.7826 (pt0) REVERT: A 257 ASN cc_start: 0.7784 (t0) cc_final: 0.7263 (t0) REVERT: A 262 ARG cc_start: 0.6598 (ttt90) cc_final: 0.6202 (ttm-80) REVERT: A 331 LEU cc_start: 0.4607 (mt) cc_final: 0.4329 (mp) REVERT: A 334 ARG cc_start: 0.6149 (tmm-80) cc_final: 0.5511 (tmm160) outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 0.2441 time to fit residues: 10.9352 Evaluate side-chains 28 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121838 restraints weight = 2369.370| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.70 r_work: 0.3161 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2318 Z= 0.206 Angle : 0.607 7.303 3151 Z= 0.298 Chirality : 0.038 0.127 381 Planarity : 0.004 0.035 383 Dihedral : 3.762 14.981 311 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.03 % Allowed : 38.31 % Favored : 57.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.52), residues: 281 helix: 1.33 (0.38), residues: 194 sheet: -1.17 (1.32), residues: 18 loop : -1.57 (0.73), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 297 HIS 0.002 0.001 HIS A 91 PHE 0.008 0.001 PHE A 269 TYR 0.012 0.001 TYR A 280 ARG 0.002 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.259 Fit side-chains REVERT: A 29 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.7189 (ttp-110) REVERT: A 200 GLN cc_start: 0.6738 (tm-30) cc_final: 0.6455 (tt0) REVERT: A 201 ARG cc_start: 0.7524 (mmm-85) cc_final: 0.6809 (ttm110) REVERT: A 262 ARG cc_start: 0.8491 (ttt90) cc_final: 0.8109 (ttm-80) REVERT: A 334 ARG cc_start: 0.7551 (tmm-80) cc_final: 0.6937 (tmm160) outliers start: 10 outliers final: 6 residues processed: 37 average time/residue: 0.1986 time to fit residues: 8.4386 Evaluate side-chains 29 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 277 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 0.0970 chunk 25 optimal weight: 0.0670 chunk 27 optimal weight: 0.0040 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.3128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125306 restraints weight = 2368.193| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.68 r_work: 0.3188 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2318 Z= 0.147 Angle : 0.534 6.690 3151 Z= 0.258 Chirality : 0.037 0.120 381 Planarity : 0.004 0.058 383 Dihedral : 3.438 14.311 311 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.23 % Allowed : 39.11 % Favored : 57.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.52), residues: 281 helix: 1.75 (0.39), residues: 192 sheet: -1.30 (1.28), residues: 18 loop : -1.64 (0.70), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.001 0.000 HIS A 91 PHE 0.011 0.001 PHE A 58 TYR 0.008 0.001 TYR A 280 ARG 0.001 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.256 Fit side-chains REVERT: A 29 ARG cc_start: 0.7438 (ttm-80) cc_final: 0.6963 (ttm170) REVERT: A 108 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8140 (tttm) REVERT: A 200 GLN cc_start: 0.6893 (tm-30) cc_final: 0.6610 (tt0) REVERT: A 201 ARG cc_start: 0.7492 (mmm-85) cc_final: 0.6829 (ttm110) REVERT: A 233 ASP cc_start: 0.7861 (m-30) cc_final: 0.7615 (m-30) REVERT: A 262 ARG cc_start: 0.8450 (ttt90) cc_final: 0.8096 (ttm-80) REVERT: A 331 LEU cc_start: 0.6780 (mt) cc_final: 0.6572 (mp) REVERT: A 334 ARG cc_start: 0.7534 (tmm-80) cc_final: 0.6913 (tmm160) outliers start: 8 outliers final: 6 residues processed: 32 average time/residue: 0.2459 time to fit residues: 8.8580 Evaluate side-chains 30 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 19 optimal weight: 0.0770 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.0060 chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.167765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122162 restraints weight = 2367.103| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.66 r_work: 0.3157 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2318 Z= 0.170 Angle : 0.528 6.664 3151 Z= 0.257 Chirality : 0.037 0.122 381 Planarity : 0.004 0.044 383 Dihedral : 3.345 14.017 311 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 6.85 % Allowed : 34.68 % Favored : 58.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.52), residues: 281 helix: 1.86 (0.39), residues: 192 sheet: -1.13 (1.31), residues: 18 loop : -1.54 (0.70), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.002 0.001 HIS A 91 PHE 0.010 0.001 PHE A 269 TYR 0.010 0.001 TYR A 280 ARG 0.001 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.254 Fit side-chains REVERT: A 29 ARG cc_start: 0.7508 (ttm-80) cc_final: 0.7066 (ttm170) REVERT: A 108 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8146 (tttm) REVERT: A 201 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.6996 (ttm110) REVERT: A 233 ASP cc_start: 0.7876 (m-30) cc_final: 0.7617 (m-30) REVERT: A 262 ARG cc_start: 0.8480 (ttt90) cc_final: 0.8086 (ttm-80) REVERT: A 334 ARG cc_start: 0.7514 (tmm-80) cc_final: 0.6968 (tmm160) outliers start: 17 outliers final: 11 residues processed: 39 average time/residue: 0.2128 time to fit residues: 9.4660 Evaluate side-chains 33 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.158277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.111508 restraints weight = 2409.162| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.71 r_work: 0.3093 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2318 Z= 0.225 Angle : 0.548 6.689 3151 Z= 0.269 Chirality : 0.038 0.122 381 Planarity : 0.004 0.040 383 Dihedral : 3.447 14.452 311 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.24 % Allowed : 36.69 % Favored : 58.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.51), residues: 281 helix: 1.68 (0.38), residues: 194 sheet: -0.99 (1.31), residues: 18 loop : -1.49 (0.71), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.002 0.001 HIS A 91 PHE 0.011 0.001 PHE A 269 TYR 0.012 0.001 TYR A 280 ARG 0.001 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.256 Fit side-chains REVERT: A 29 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7108 (ttm170) REVERT: A 201 ARG cc_start: 0.7685 (mmm-85) cc_final: 0.7119 (ttm110) REVERT: A 334 ARG cc_start: 0.7445 (tmm-80) cc_final: 0.6871 (tmm160) outliers start: 13 outliers final: 12 residues processed: 35 average time/residue: 0.2088 time to fit residues: 8.4548 Evaluate side-chains 34 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.159149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114105 restraints weight = 2369.729| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.68 r_work: 0.3128 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2318 Z= 0.183 Angle : 0.537 7.822 3151 Z= 0.257 Chirality : 0.037 0.121 381 Planarity : 0.004 0.036 383 Dihedral : 3.310 14.354 311 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.24 % Allowed : 35.89 % Favored : 58.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.51), residues: 281 helix: 1.81 (0.38), residues: 194 sheet: -1.06 (1.30), residues: 18 loop : -1.44 (0.71), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.002 0.001 HIS A 91 PHE 0.009 0.001 PHE A 269 TYR 0.010 0.001 TYR A 280 ARG 0.002 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.248 Fit side-chains REVERT: A 201 ARG cc_start: 0.7652 (mmm-85) cc_final: 0.7070 (ttm110) REVERT: A 233 ASP cc_start: 0.7992 (m-30) cc_final: 0.7730 (m-30) REVERT: A 334 ARG cc_start: 0.7480 (tmm-80) cc_final: 0.6914 (tmm160) outliers start: 13 outliers final: 11 residues processed: 37 average time/residue: 0.2106 time to fit residues: 8.9739 Evaluate side-chains 35 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.3980 chunk 22 optimal weight: 0.0470 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.160499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115567 restraints weight = 2421.448| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.70 r_work: 0.3150 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2318 Z= 0.167 Angle : 0.526 6.981 3151 Z= 0.251 Chirality : 0.037 0.120 381 Planarity : 0.004 0.034 383 Dihedral : 3.181 14.223 311 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.24 % Allowed : 35.89 % Favored : 58.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.52), residues: 281 helix: 1.98 (0.38), residues: 194 sheet: -0.99 (1.29), residues: 18 loop : -1.44 (0.70), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.001 0.001 HIS A 91 PHE 0.009 0.001 PHE A 269 TYR 0.009 0.001 TYR A 280 ARG 0.001 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.243 Fit side-chains REVERT: A 201 ARG cc_start: 0.7666 (mmm-85) cc_final: 0.7075 (ttm110) REVERT: A 233 ASP cc_start: 0.7828 (m-30) cc_final: 0.7568 (m-30) REVERT: A 334 ARG cc_start: 0.7471 (tmm-80) cc_final: 0.6900 (tmm160) outliers start: 13 outliers final: 12 residues processed: 36 average time/residue: 0.2195 time to fit residues: 9.0314 Evaluate side-chains 36 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.159074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113691 restraints weight = 2466.498| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.73 r_work: 0.3126 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2318 Z= 0.192 Angle : 0.537 6.845 3151 Z= 0.258 Chirality : 0.037 0.122 381 Planarity : 0.004 0.033 383 Dihedral : 3.269 14.088 311 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.65 % Allowed : 35.48 % Favored : 58.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.51), residues: 281 helix: 2.00 (0.38), residues: 192 sheet: -0.82 (1.28), residues: 18 loop : -1.61 (0.69), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.002 0.001 HIS A 91 PHE 0.010 0.001 PHE A 269 TYR 0.011 0.001 TYR A 280 ARG 0.001 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.238 Fit side-chains REVERT: A 201 ARG cc_start: 0.7698 (mmm-85) cc_final: 0.7129 (ttm110) REVERT: A 233 ASP cc_start: 0.8014 (m-30) cc_final: 0.7750 (m-30) REVERT: A 334 ARG cc_start: 0.7478 (tmm-80) cc_final: 0.6900 (tmm160) outliers start: 14 outliers final: 14 residues processed: 36 average time/residue: 0.2010 time to fit residues: 8.2961 Evaluate side-chains 37 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 0.0010 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.167534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122276 restraints weight = 2394.629| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.68 r_work: 0.3156 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2318 Z= 0.177 Angle : 0.525 6.539 3151 Z= 0.252 Chirality : 0.037 0.121 381 Planarity : 0.004 0.033 383 Dihedral : 3.227 13.971 311 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.65 % Allowed : 35.89 % Favored : 58.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.51), residues: 281 helix: 2.10 (0.38), residues: 192 sheet: -0.70 (1.28), residues: 18 loop : -1.61 (0.68), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.002 0.001 HIS A 91 PHE 0.009 0.001 PHE A 269 TYR 0.011 0.001 TYR A 280 ARG 0.001 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 21 time to evaluate : 0.237 Fit side-chains REVERT: A 201 ARG cc_start: 0.7703 (mmm-85) cc_final: 0.7138 (ttm110) REVERT: A 233 ASP cc_start: 0.7989 (m-30) cc_final: 0.7727 (m-30) REVERT: A 334 ARG cc_start: 0.7506 (tmm-80) cc_final: 0.6978 (tmm160) outliers start: 14 outliers final: 13 residues processed: 34 average time/residue: 0.1584 time to fit residues: 6.5198 Evaluate side-chains 34 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.167011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121596 restraints weight = 2380.454| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.69 r_work: 0.3147 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2318 Z= 0.186 Angle : 0.531 6.506 3151 Z= 0.256 Chirality : 0.037 0.121 381 Planarity : 0.004 0.033 383 Dihedral : 3.274 14.084 311 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.65 % Allowed : 35.89 % Favored : 58.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.51), residues: 281 helix: 2.09 (0.38), residues: 192 sheet: -0.77 (1.28), residues: 18 loop : -1.61 (0.69), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.002 0.001 HIS A 91 PHE 0.010 0.001 PHE A 269 TYR 0.011 0.001 TYR A 280 ARG 0.001 0.000 ARG A 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 21 time to evaluate : 0.245 Fit side-chains REVERT: A 201 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.7144 (ttm110) REVERT: A 233 ASP cc_start: 0.8001 (m-30) cc_final: 0.7739 (m-30) REVERT: A 334 ARG cc_start: 0.7482 (tmm-80) cc_final: 0.6957 (tmm160) outliers start: 14 outliers final: 14 residues processed: 34 average time/residue: 0.1506 time to fit residues: 6.1043 Evaluate side-chains 35 residues out of total 266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 21 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.167887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123974 restraints weight = 2365.372| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.62 r_work: 0.3159 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2318 Z= 0.170 Angle : 0.519 6.491 3151 Z= 0.250 Chirality : 0.037 0.119 381 Planarity : 0.004 0.033 383 Dihedral : 3.209 13.933 311 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 6.45 % Allowed : 34.68 % Favored : 58.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.52), residues: 281 helix: 2.15 (0.38), residues: 192 sheet: -0.80 (1.27), residues: 18 loop : -1.60 (0.69), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.002 0.001 HIS A 91 PHE 0.009 0.001 PHE A 269 TYR 0.010 0.001 TYR A 280 ARG 0.001 0.000 ARG A 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1692.26 seconds wall clock time: 30 minutes 40.80 seconds (1840.80 seconds total)